## Version Release Notes

First version: 08.24.2012
Current version: 10.15.2018

New in version 12.27.2017:

• A version that works using Matlab Runtime Environment (no Matlab license required) is released.
• Fixes to work correctly on Ubuntu machines

New in version 01.24.2014:

• Reworked the structure of the script into procedure-based
• The script now accepts multiple scans to process with the same parameters.
• The following modes of face masking are allowed by script
1. based on FSL-coregistered coordinates file (generated by fsl after coregistration)
2. based on supplied ROI coordinate file
3. based on explicitly supplied ROI coordinates
4. based on the reference scan
• 3D snapshots
• tweaked brain mask application to exclude more boundary voxels
• better support of anisotropic voxels
• new parameters:
• ref: reference scan
• use_manual_roi: signal that manual ROI will be used instead of auto-registration.
• rois: specification of manual ROI’s
• dirs: ROI normal direction (s)
• step 0: scan lists are converted to be used with xnat2loc
• new face masking script takes a list of scans, reference and ROI parameters as input.

## Usage

mask_face <image>[,<image>..] [options]

The first argument must list one or more MR head image files. If more than one image is specified, you must also specify one of them as reference with -r option. The reference image will be used for spatial co-registration with an atlas, and others will use the reference facial mask.

By default, the input is the DICOM directory of a single series. You can also supply images in Analyze/NIFTI (.hdr/.img pair) format by adding -a option. The output and input formats are the same.

## Options

For the complete set of options, run mask_face without parameters.

FlagDescription
-aRequired if you are supplying images in Analyze/NIFTI (.hdr/.img pair) format
-m <method>

Method used (coating, blur, normfilter, all):

• coating: sets all voxels in the face layer to the single average intensity
• blur: performs the entire volume blur, and limit the effect to the facial region
• normfilter: (recommended) a fine-tuned method that will preserve most of the intensity distribution
• all: produces output by all three methods
-t <threshold>

Mask threshold: Threshold is selected automatically (recommended), but can be changed with this option

-s <grid_step>Grid Step: Larger grid step will result in coarser looking 3D renderings, and tends to modify more voxels outside of the immediate near-surface
-v <#>

Control the amount of intermediate output:

• 0: only saves the resulting output
• 2: will generate the 3D volumes for boundary layer, boundary mask, and “flattened” face (both blurred and unblurred)
-bGenerate the brain mask used by FSL's bet algorithm prior to face masking and use it to exclude brain voxels from modification
-e <#>